Quality control (QC) analyses were performed using PLINK v1.0723 and EIGENSTRAT24. In addition to standard QC protocols, particular detail focused on cross-platform comparisons of concordance, allele frequency and differential missingness, given the use of control samples genotyped previously on different Illumina platforms (full details and ordered QC pipeline available online, Figure S1). In general, two thresholds were used for SNP QC: a more stringent threshold at which SNPs were removed, and a second liberalized threshold for which SNPs were flagged and re-examined later for potential QC-related bias. All flagged SNPs with p<1×10−3 in any analysis are annotated in Tables S2-S4.
